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' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ), 'gf_id' => 'HOM05D001194', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001194' ), 'data_identifier' => 'HOM05D001194', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ) $gf_id = 'HOM05D001194' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001194' ) $data_identifier = 'HOM05D001194' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 17, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 8, 'sgi' => (int) 7, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356690' $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' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ), 'gf_id' => 'HOM05D001194', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001194' ), 'data_identifier' => 'HOM05D001194', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ) $gf_id = 'HOM05D001194' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001194' ) $data_identifier = 'HOM05D001194' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 17, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 8, 'sgi' => (int) 7, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356690' $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' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ), 'gf_id' => 'HOM05D001194', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001194' ), 'data_identifier' => 'HOM05D001194', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ) $gf_id = 'HOM05D001194' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001194' ) $data_identifier = 'HOM05D001194' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 17, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 8, 'sgi' => (int) 7, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356690' $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' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ), 'gf_id' => 'HOM05D001194', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001194' ), 'data_identifier' => 'HOM05D001194', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ) $gf_id = 'HOM05D001194' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001194' ) $data_identifier = 'HOM05D001194' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 17, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 8, 'sgi' => (int) 7, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356690' $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' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ), 'gf_id' => 'HOM05D001194', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001194' ), 'data_identifier' => 'HOM05D001194', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ) $gf_id = 'HOM05D001194' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001194' ) $data_identifier = 'HOM05D001194' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 17, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 8, 'sgi' => (int) 7, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356690' $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' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ), 'gf_id' => 'HOM05D001194', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001194' ), 'data_identifier' => 'HOM05D001194', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ) $gf_id = 'HOM05D001194' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001194' ) $data_identifier = 'HOM05D001194' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 17, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 8, 'sgi' => (int) 7, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356690' $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' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ), 'gf_id' => 'HOM05D001194', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001194' ), 'data_identifier' => 'HOM05D001194', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ) $gf_id = 'HOM05D001194' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001194' ) $data_identifier = 'HOM05D001194' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 17, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 8, 'sgi' => (int) 7, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356690' $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' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ), 'gf_id' => 'HOM05D001194', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001194' ), 'data_identifier' => 'HOM05D001194', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ) $gf_id = 'HOM05D001194' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001194' ) $data_identifier = 'HOM05D001194' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 17, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 8, 'sgi' => (int) 7, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356690' $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' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ), 'gf_id' => 'HOM05D001194', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001194' ), 'data_identifier' => 'HOM05D001194', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ) $gf_id = 'HOM05D001194' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001194' ) $data_identifier = 'HOM05D001194' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 17, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 8, 'sgi' => (int) 7, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356690' $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' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ), 'gf_id' => 'HOM05D001194', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001194' ), 'data_identifier' => 'HOM05D001194', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ) $gf_id = 'HOM05D001194' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001194' ) $data_identifier = 'HOM05D001194' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 17, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 8, 'sgi' => (int) 7, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356690' $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' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ), 'gf_id' => 'HOM05D001194', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001194' ), 'data_identifier' => 'HOM05D001194', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ) $gf_id = 'HOM05D001194' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001194' ) $data_identifier = 'HOM05D001194' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 17, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 8, 'sgi' => (int) 7, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356690' $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' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ), 'gf_id' => 'HOM05D001194', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001194' ), 'data_identifier' => 'HOM05D001194', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ) $gf_id = 'HOM05D001194' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001194' ) $data_identifier = 'HOM05D001194' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 17, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 8, 'sgi' => (int) 7, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356690' $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' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ), 'gf_id' => 'HOM05D001194', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001194' ), 'data_identifier' => 'HOM05D001194', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ) $gf_id = 'HOM05D001194' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001194' ) $data_identifier = 'HOM05D001194' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 17, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 8, 'sgi' => (int) 7, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356690' $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' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ), 'gf_id' => 'HOM05D001194', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001194' ), 'data_identifier' => 'HOM05D001194', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ) $gf_id = 'HOM05D001194' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001194' ) $data_identifier = 'HOM05D001194' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 17, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 8, 'sgi' => (int) 7, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356690' $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' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ), 'gf_id' => 'HOM05D001194', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001194' ), 'data_identifier' => 'HOM05D001194', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ) $gf_id = 'HOM05D001194' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001194' ) $data_identifier = 'HOM05D001194' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 17, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 8, 'sgi' => (int) 7, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356690' $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' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ), 'gf_id' => 'HOM05D001194', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001194' ), 'data_identifier' => 'HOM05D001194', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ) $gf_id = 'HOM05D001194' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001194' ) $data_identifier = 'HOM05D001194' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 17, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 8, 'sgi' => (int) 7, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356690' $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' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ), 'gf_id' => 'HOM05D001194', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001194' ), 'data_identifier' => 'HOM05D001194', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ) $gf_id = 'HOM05D001194' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001194' ) $data_identifier = 'HOM05D001194' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 17, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 8, 'sgi' => (int) 7, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356690' $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' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ), 'gf_id' => 'HOM05D001194', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001194' ), 'data_identifier' => 'HOM05D001194', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ) $gf_id = 'HOM05D001194' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001194' ) $data_identifier = 'HOM05D001194' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 17, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 8, 'sgi' => (int) 7, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356690' $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' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ), 'gf_id' => 'HOM05D001194', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001194' ), 'data_identifier' => 'HOM05D001194', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ) $gf_id = 'HOM05D001194' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001194' ) $data_identifier = 'HOM05D001194' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 17, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 8, 'sgi' => (int) 7, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356690' $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' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ), 'gf_id' => 'HOM05D001194', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001194' ), 'data_identifier' => 'HOM05D001194', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ) $gf_id = 'HOM05D001194' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001194' ) $data_identifier = 'HOM05D001194' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 17, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 8, 'sgi' => (int) 7, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356690' $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' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ), 'gf_id' => 'HOM05D001194', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001194' ), 'data_identifier' => 'HOM05D001194', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ) $gf_id = 'HOM05D001194' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001194' ) $data_identifier = 'HOM05D001194' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 17, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 8, 'sgi' => (int) 7, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356690' $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' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ), 'gf_id' => 'HOM05D001194', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001194' ), 'data_identifier' => 'HOM05D001194', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ) $gf_id = 'HOM05D001194' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001194' ) $data_identifier = 'HOM05D001194' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 17, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 8, 'sgi' => (int) 7, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356690' $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' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ), 'gf_id' => 'HOM05D001194', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001194' ), 'data_identifier' => 'HOM05D001194', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ) $gf_id = 'HOM05D001194' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001194' ) $data_identifier = 'HOM05D001194' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 17, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 8, 'sgi' => (int) 7, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356690' $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' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ), 'gf_id' => 'HOM05D001194', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001194' ), 'data_identifier' => 'HOM05D001194', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ) $gf_id = 'HOM05D001194' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001194' ) $data_identifier = 'HOM05D001194' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 17, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 8, 'sgi' => (int) 7, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356690' $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' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ), 'gf_id' => 'HOM05D001194', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001194' ), 'data_identifier' => 'HOM05D001194', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ) $gf_id = 'HOM05D001194' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001194' ) $data_identifier = 'HOM05D001194' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 17, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 8, 'sgi' => (int) 7, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356690' $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' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ), 'gf_id' => 'HOM05D001194', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001194' ), 'data_identifier' => 'HOM05D001194', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ) $gf_id = 'HOM05D001194' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001194' ) $data_identifier = 'HOM05D001194' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 17, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 8, 'sgi' => (int) 7, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356690' $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' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ), 'gf_id' => 'HOM05D001194', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001194' ), 'data_identifier' => 'HOM05D001194', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ) $gf_id = 'HOM05D001194' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001194' ) $data_identifier = 'HOM05D001194' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 17, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 8, 'sgi' => (int) 7, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356690' $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' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ), 'gf_id' => 'HOM05D001194', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001194' ), 'data_identifier' => 'HOM05D001194', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ) $gf_id = 'HOM05D001194' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001194' ) $data_identifier = 'HOM05D001194' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 17, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 8, 'sgi' => (int) 7, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356690' $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' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ), 'gf_id' => 'HOM05D001194', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001194' ), 'data_identifier' => 'HOM05D001194', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ) $gf_id = 'HOM05D001194' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001194' ) $data_identifier = 'HOM05D001194' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 17, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 8, 'sgi' => (int) 7, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356690' $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' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ), 'gf_id' => 'HOM05D001194', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001194' ), 'data_identifier' => 'HOM05D001194', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ) $gf_id = 'HOM05D001194' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001194' ) $data_identifier = 'HOM05D001194' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 17, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 8, 'sgi' => (int) 7, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356690' $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' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ), 'gf_id' => 'HOM05D001194', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001194' ), 'data_identifier' => 'HOM05D001194', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ) $gf_id = 'HOM05D001194' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001194' ) $data_identifier = 'HOM05D001194' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 17, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 8, 'sgi' => (int) 7, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356690' $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' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ), 'gf_id' => 'HOM05D001194', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001194' ), 'data_identifier' => 'HOM05D001194', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ) $gf_id = 'HOM05D001194' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001194' ) $data_identifier = 'HOM05D001194' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 17, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 8, 'sgi' => (int) 7, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356690' $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' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ), 'gf_id' => 'HOM05D001194', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001194' ), 'data_identifier' => 'HOM05D001194', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ) $gf_id = 'HOM05D001194' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001194' ) $data_identifier = 'HOM05D001194' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 17, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 8, 'sgi' => (int) 7, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356690' $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' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ), 'gf_id' => 'HOM05D001194', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001194' ), 'data_identifier' => 'HOM05D001194', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ) $gf_id = 'HOM05D001194' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001194' ) $data_identifier = 'HOM05D001194' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 17, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 8, 'sgi' => (int) 7, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356690' $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' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ), 'gf_id' => 'HOM05D001194', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001194' ), 'data_identifier' => 'HOM05D001194', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ) $gf_id = 'HOM05D001194' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001194' ) $data_identifier = 'HOM05D001194' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 17, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 8, 'sgi' => (int) 7, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356690' $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' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ), 'gf_id' => 'HOM05D001194', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001194' ), 'data_identifier' => 'HOM05D001194', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ) $gf_id = 'HOM05D001194' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001194' ) $data_identifier = 'HOM05D001194' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 17, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 8, 'sgi' => (int) 7, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356690' $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' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ), 'gf_id' => 'HOM05D001194', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001194' ), 'data_identifier' => 'HOM05D001194', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ) $gf_id = 'HOM05D001194' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001194' ) $data_identifier = 'HOM05D001194' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 17, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 8, 'sgi' => (int) 7, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356690' $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' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ), 'gf_id' => 'HOM05D001194', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001194' ), 'data_identifier' => 'HOM05D001194', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ) $gf_id = 'HOM05D001194' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001194' ) $data_identifier = 'HOM05D001194' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 17, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 8, 'sgi' => (int) 7, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356690' $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' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ), 'gf_id' => 'HOM05D001194', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001194' ), 'data_identifier' => 'HOM05D001194', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ) $gf_id = 'HOM05D001194' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001194' ) $data_identifier = 'HOM05D001194' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 17, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 8, 'sgi' => (int) 7, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356690' $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' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ), 'gf_id' => 'HOM05D001194', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001194' ), 'data_identifier' => 'HOM05D001194', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ) $gf_id = 'HOM05D001194' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001194' ) $data_identifier = 'HOM05D001194' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 17, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 8, 'sgi' => (int) 7, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356690' $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' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ), 'gf_id' => 'HOM05D001194', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001194' ), 'data_identifier' => 'HOM05D001194', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ) $gf_id = 'HOM05D001194' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001194' ) $data_identifier = 'HOM05D001194' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 17, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 8, 'sgi' => (int) 7, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356690' $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' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ), 'gf_id' => 'HOM05D001194', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001194' ), 'data_identifier' => 'HOM05D001194', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ) $gf_id = 'HOM05D001194' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001194' ) $data_identifier = 'HOM05D001194' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 17, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 8, 'sgi' => (int) 7, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356690' $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' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ), 'gf_id' => 'HOM05D001194', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001194' ), 'data_identifier' => 'HOM05D001194', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ) $gf_id = 'HOM05D001194' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001194' ) $data_identifier = 'HOM05D001194' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 17, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 8, 'sgi' => (int) 7, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356690' $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' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ), 'gf_id' => 'HOM05D001194', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001194' ), 'data_identifier' => 'HOM05D001194', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ) $gf_id = 'HOM05D001194' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001194' ) $data_identifier = 'HOM05D001194' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 17, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 8, 'sgi' => (int) 7, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356690' $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' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ), 'gf_id' => 'HOM05D001194', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001194' ), 'data_identifier' => 'HOM05D001194', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ) $gf_id = 'HOM05D001194' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001194' ) $data_identifier = 'HOM05D001194' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 17, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 8, 'sgi' => (int) 7, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356690' $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' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ), 'gf_id' => 'HOM05D001194', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001194' ), 'data_identifier' => 'HOM05D001194', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ) $gf_id = 'HOM05D001194' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001194' ) $data_identifier = 'HOM05D001194' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 17, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 8, 'sgi' => (int) 7, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356690' $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' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ), 'gf_id' => 'HOM05D001194', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001194' ), 'data_identifier' => 'HOM05D001194', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ) $gf_id = 'HOM05D001194' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001194' ) $data_identifier = 'HOM05D001194' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 17, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 8, 'sgi' => (int) 7, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356690' $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' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ), 'gf_id' => 'HOM05D001194', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001194' ), 'data_identifier' => 'HOM05D001194', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ) $gf_id = 'HOM05D001194' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001194' ) $data_identifier = 'HOM05D001194' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 17, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 8, 'sgi' => (int) 7, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356690' $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' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ), 'gf_id' => 'HOM05D001194', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001194' ), 'data_identifier' => 'HOM05D001194', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ) $gf_id = 'HOM05D001194' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001194' ) $data_identifier = 'HOM05D001194' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 17, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 8, 'sgi' => (int) 7, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356690' $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' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ), 'gf_id' => 'HOM05D001194', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001194' ), 'data_identifier' => 'HOM05D001194', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ) $gf_id = 'HOM05D001194' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001194' ) $data_identifier = 'HOM05D001194' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 17, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 8, 'sgi' => (int) 7, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356690' $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' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ), 'gf_id' => 'HOM05D001194', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001194' ), 'data_identifier' => 'HOM05D001194', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ) $gf_id = 'HOM05D001194' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001194' ) $data_identifier = 'HOM05D001194' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 17, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 8, 'sgi' => (int) 7, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356690' $species_info = array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ) $local_species = 'cqu' $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' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ), 'gf_id' => 'HOM05D001194', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001194' ), 'data_identifier' => 'HOM05D001194', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ) $gf_id = 'HOM05D001194' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001194' ) $data_identifier = 'HOM05D001194' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 17, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 8, 'sgi' => (int) 7, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356690' $species_info = array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ) $local_species = 'cqu' $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' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ), 'gf_id' => 'HOM05D001194', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001194' ), 'data_identifier' => 'HOM05D001194', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ) $gf_id = 'HOM05D001194' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001194' ) $data_identifier = 'HOM05D001194' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 17, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 8, 'sgi' => (int) 7, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356690' $species_info = array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ) $local_species = 'car' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ), 'gf_id' => 'HOM05D001194', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001194' ), 'data_identifier' => 'HOM05D001194', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ) $gf_id = 'HOM05D001194' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001194' ) $data_identifier = 'HOM05D001194' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 17, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 8, 'sgi' => (int) 7, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356690' $species_info = array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ) $local_species = 'car' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ), 'gf_id' => 'HOM05D001194', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001194' ), 'data_identifier' => 'HOM05D001194', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ) $gf_id = 'HOM05D001194' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001194' ) $data_identifier = 'HOM05D001194' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 17, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 8, 'sgi' => (int) 7, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356690' $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' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ), 'gf_id' => 'HOM05D001194', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001194' ), 'data_identifier' => 'HOM05D001194', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ) $gf_id = 'HOM05D001194' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001194' ) $data_identifier = 'HOM05D001194' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 17, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 8, 'sgi' => (int) 7, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356690' $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' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ), 'gf_id' => 'HOM05D001194', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001194' ), 'data_identifier' => 'HOM05D001194', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ) $gf_id = 'HOM05D001194' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001194' ) $data_identifier = 'HOM05D001194' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 17, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 8, 'sgi' => (int) 7, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356690' $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' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ), 'gf_id' => 'HOM05D001194', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001194' ), 'data_identifier' => 'HOM05D001194', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ) $gf_id = 'HOM05D001194' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001194' ) $data_identifier = 'HOM05D001194' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 17, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 8, 'sgi' => (int) 7, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356690' $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' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ), 'gf_id' => 'HOM05D001194', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001194' ), 'data_identifier' => 'HOM05D001194', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ) $gf_id = 'HOM05D001194' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001194' ) $data_identifier = 'HOM05D001194' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 17, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 8, 'sgi' => (int) 7, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356690' $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' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ), 'gf_id' => 'HOM05D001194', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001194' ), 'data_identifier' => 'HOM05D001194', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ) $gf_id = 'HOM05D001194' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001194' ) $data_identifier = 'HOM05D001194' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 17, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 8, 'sgi' => (int) 7, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356690' $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' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ), 'gf_id' => 'HOM05D001194', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001194' ), 'data_identifier' => 'HOM05D001194', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ) $gf_id = 'HOM05D001194' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001194' ) $data_identifier = 'HOM05D001194' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 17, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 8, 'sgi' => (int) 7, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356690' $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' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ), 'gf_id' => 'HOM05D001194', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001194' ), 'data_identifier' => 'HOM05D001194', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ) $gf_id = 'HOM05D001194' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001194' ) $data_identifier = 'HOM05D001194' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 17, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 8, 'sgi' => (int) 7, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356690' $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' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ), 'gf_id' => 'HOM05D001194', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001194' ), 'data_identifier' => 'HOM05D001194', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ) $gf_id = 'HOM05D001194' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001194' ) $data_identifier = 'HOM05D001194' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 17, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 8, 'sgi' => (int) 7, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356690' $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' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ), 'gf_id' => 'HOM05D001194', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001194' ), 'data_identifier' => 'HOM05D001194', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ) $gf_id = 'HOM05D001194' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001194' ) $data_identifier = 'HOM05D001194' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 17, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 8, 'sgi' => (int) 7, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356690' $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' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ), 'gf_id' => 'HOM05D001194', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001194' ), 'data_identifier' => 'HOM05D001194', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ) $gf_id = 'HOM05D001194' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001194' ) $data_identifier = 'HOM05D001194' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 17, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 8, 'sgi' => (int) 7, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356690' $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' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ), 'gf_id' => 'HOM05D001194', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001194' ), 'data_identifier' => 'HOM05D001194', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ) $gf_id = 'HOM05D001194' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001194' ) $data_identifier = 'HOM05D001194' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 17, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 8, 'sgi' => (int) 7, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356690' $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' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ), 'gf_id' => 'HOM05D001194', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001194' ), 'data_identifier' => 'HOM05D001194', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ) $gf_id = 'HOM05D001194' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001194' ) $data_identifier = 'HOM05D001194' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 17, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 8, 'sgi' => (int) 7, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356690' $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' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ), 'gf_id' => 'HOM05D001194', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001194' ), 'data_identifier' => 'HOM05D001194', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ) $gf_id = 'HOM05D001194' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001194' ) $data_identifier = 'HOM05D001194' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 17, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 8, 'sgi' => (int) 7, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356690' $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' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ), 'gf_id' => 'HOM05D001194', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001194' ), 'data_identifier' => 'HOM05D001194', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ) $gf_id = 'HOM05D001194' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001194' ) $data_identifier = 'HOM05D001194' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 17, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 8, 'sgi' => (int) 7, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356690' $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' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ), 'gf_id' => 'HOM05D001194', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001194' ), 'data_identifier' => 'HOM05D001194', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ) $gf_id = 'HOM05D001194' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001194' ) $data_identifier = 'HOM05D001194' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 17, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 8, 'sgi' => (int) 7, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356690' $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' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ), 'gf_id' => 'HOM05D001194', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001194' ), 'data_identifier' => 'HOM05D001194', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ) $gf_id = 'HOM05D001194' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001194' ) $data_identifier = 'HOM05D001194' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 17, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 8, 'sgi' => (int) 7, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356690' $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' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ), 'gf_id' => 'HOM05D001194', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001194' ), 'data_identifier' => 'HOM05D001194', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ) $gf_id = 'HOM05D001194' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001194' ) $data_identifier = 'HOM05D001194' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 17, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 8, 'sgi' => (int) 7, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356690' $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' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ), 'gf_id' => 'HOM05D001194', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001194' ), 'data_identifier' => 'HOM05D001194', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ) $gf_id = 'HOM05D001194' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001194' ) $data_identifier = 'HOM05D001194' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 17, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 8, 'sgi' => (int) 7, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356690' $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' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ), 'gf_id' => 'HOM05D001194', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001194' ), 'data_identifier' => 'HOM05D001194', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ) $gf_id = 'HOM05D001194' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001194' ) $data_identifier = 'HOM05D001194' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 17, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 8, 'sgi' => (int) 7, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356690' $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' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ), 'gf_id' => 'HOM05D001194', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001194' ), 'data_identifier' => 'HOM05D001194', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ) $gf_id = 'HOM05D001194' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001194' ) $data_identifier = 'HOM05D001194' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 17, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 8, 'sgi' => (int) 7, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356690' $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' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ), 'gf_id' => 'HOM05D001194', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001194' ), 'data_identifier' => 'HOM05D001194', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ) $gf_id = 'HOM05D001194' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001194' ) $data_identifier = 'HOM05D001194' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 17, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 8, 'sgi' => (int) 7, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356690' $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' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ), 'gf_id' => 'HOM05D001194', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001194' ), 'data_identifier' => 'HOM05D001194', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ) $gf_id = 'HOM05D001194' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001194' ) $data_identifier = 'HOM05D001194' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 17, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 8, 'sgi' => (int) 7, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356690' $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' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ), 'gf_id' => 'HOM05D001194', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001194' ), 'data_identifier' => 'HOM05D001194', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ) $gf_id = 'HOM05D001194' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001194' ) $data_identifier = 'HOM05D001194' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 17, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 8, 'sgi' => (int) 7, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356690' $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' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ), 'gf_id' => 'HOM05D001194', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001194' ), 'data_identifier' => 'HOM05D001194', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ) $gf_id = 'HOM05D001194' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001194' ) $data_identifier = 'HOM05D001194' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 17, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 8, 'sgi' => (int) 7, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356690' $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' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ), 'gf_id' => 'HOM05D001194', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001194' ), 'data_identifier' => 'HOM05D001194', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ) $gf_id = 'HOM05D001194' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001194' ) $data_identifier = 'HOM05D001194' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 17, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 8, 'sgi' => (int) 7, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356690' $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' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ), 'gf_id' => 'HOM05D001194', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001194' ), 'data_identifier' => 'HOM05D001194', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ) $gf_id = 'HOM05D001194' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001194' ) $data_identifier = 'HOM05D001194' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 17, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 8, 'sgi' => (int) 7, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356690' $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' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ), 'gf_id' => 'HOM05D001194', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001194' ), 'data_identifier' => 'HOM05D001194', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ) $gf_id = 'HOM05D001194' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001194' ) $data_identifier = 'HOM05D001194' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 17, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 8, 'sgi' => (int) 7, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356690' $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' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ), 'gf_id' => 'HOM05D001194', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001194' ), 'data_identifier' => 'HOM05D001194', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ) $gf_id = 'HOM05D001194' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001194' ) $data_identifier = 'HOM05D001194' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 17, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 8, 'sgi' => (int) 7, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356690' $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' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ), 'gf_id' => 'HOM05D001194', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001194' ), 'data_identifier' => 'HOM05D001194', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ) $gf_id = 'HOM05D001194' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001194' ) $data_identifier = 'HOM05D001194' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 17, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 8, 'sgi' => (int) 7, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356690' $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' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ), 'gf_id' => 'HOM05D001194', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001194' ), 'data_identifier' => 'HOM05D001194', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ) $gf_id = 'HOM05D001194' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001194' ) $data_identifier = 'HOM05D001194' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 17, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 8, 'sgi' => (int) 7, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356690' $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' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ), 'gf_id' => 'HOM05D001194', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001194' ), 'data_identifier' => 'HOM05D001194', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ) $gf_id = 'HOM05D001194' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001194' ) $data_identifier = 'HOM05D001194' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 17, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 8, 'sgi' => (int) 7, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356690' $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' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ), 'gf_id' => 'HOM05D001194', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001194' ), 'data_identifier' => 'HOM05D001194', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ) $gf_id = 'HOM05D001194' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001194' ) $data_identifier = 'HOM05D001194' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 17, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 8, 'sgi' => (int) 7, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356690' $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' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ), 'gf_id' => 'HOM05D001194', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001194' ), 'data_identifier' => 'HOM05D001194', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ) $gf_id = 'HOM05D001194' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001194' ) $data_identifier = 'HOM05D001194' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 17, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 8, 'sgi' => (int) 7, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356690' $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' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ), 'gf_id' => 'HOM05D001194', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001194' ), 'data_identifier' => 'HOM05D001194', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ) $gf_id = 'HOM05D001194' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001194' ) $data_identifier = 'HOM05D001194' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 17, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 8, 'sgi' => (int) 7, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356690' $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' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ), 'gf_id' => 'HOM05D001194', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001194' ), 'data_identifier' => 'HOM05D001194', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ) $gf_id = 'HOM05D001194' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001194' ) $data_identifier = 'HOM05D001194' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 17, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 8, 'sgi' => (int) 7, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356690' $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' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ), 'gf_id' => 'HOM05D001194', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001194' ), 'data_identifier' => 'HOM05D001194', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ) $gf_id = 'HOM05D001194' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001194' ) $data_identifier = 'HOM05D001194' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 17, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 8, 'sgi' => (int) 7, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356690' $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' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ), 'gf_id' => 'HOM05D001194', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001194' ), 'data_identifier' => 'HOM05D001194', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ) $gf_id = 'HOM05D001194' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001194' ) $data_identifier = 'HOM05D001194' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 17, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 8, 'sgi' => (int) 7, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356690' $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' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ), 'gf_id' => 'HOM05D001194', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001194' ), 'data_identifier' => 'HOM05D001194', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ) $gf_id = 'HOM05D001194' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001194' ) $data_identifier = 'HOM05D001194' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 17, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 8, 'sgi' => (int) 7, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356690' $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' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ), 'gf_id' => 'HOM05D001194', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001194' ), 'data_identifier' => 'HOM05D001194', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ) $gf_id = 'HOM05D001194' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001194' ) $data_identifier = 'HOM05D001194' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 17, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 8, 'sgi' => (int) 7, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356690' $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' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ), 'gf_id' => 'HOM05D001194', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001194' ), 'data_identifier' => 'HOM05D001194', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ) $gf_id = 'HOM05D001194' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001194' ) $data_identifier = 'HOM05D001194' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 17, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 8, 'sgi' => (int) 7, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356690' $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' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ), 'gf_id' => 'HOM05D001194', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001194' ), 'data_identifier' => 'HOM05D001194', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ) $gf_id = 'HOM05D001194' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001194' ) $data_identifier = 'HOM05D001194' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 17, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 8, 'sgi' => (int) 7, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356690' $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' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ), 'gf_id' => 'HOM05D001194', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001194' ), 'data_identifier' => 'HOM05D001194', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ) $gf_id = 'HOM05D001194' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001194' ) $data_identifier = 'HOM05D001194' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 17, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 8, 'sgi' => (int) 7, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356690' $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' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ), 'gf_id' => 'HOM05D001194', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001194' ), 'data_identifier' => 'HOM05D001194', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ) $gf_id = 'HOM05D001194' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001194' ) $data_identifier = 'HOM05D001194' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 17, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 8, 'sgi' => (int) 7, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356690' $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' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ), 'gf_id' => 'HOM05D001194', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001194' ), 'data_identifier' => 'HOM05D001194', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ) $gf_id = 'HOM05D001194' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001194' ) $data_identifier = 'HOM05D001194' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 17, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 8, 'sgi' => (int) 7, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356690' $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' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ), 'gf_id' => 'HOM05D001194', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001194' ), 'data_identifier' => 'HOM05D001194', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ) $gf_id = 'HOM05D001194' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001194' ) $data_identifier = 'HOM05D001194' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 17, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 8, 'sgi' => (int) 7, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356690' $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' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ), 'gf_id' => 'HOM05D001194', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001194' ), 'data_identifier' => 'HOM05D001194', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ) $gf_id = 'HOM05D001194' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001194' ) $data_identifier = 'HOM05D001194' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 17, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 8, 'sgi' => (int) 7, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356690' $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' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ), 'gf_id' => 'HOM05D001194', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001194' ), 'data_identifier' => 'HOM05D001194', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ) $gf_id = 'HOM05D001194' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001194' ) $data_identifier = 'HOM05D001194' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 17, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 8, 'sgi' => (int) 7, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356690' $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' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ), 'gf_id' => 'HOM05D001194', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001194' ), 'data_identifier' => 'HOM05D001194', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ) $gf_id = 'HOM05D001194' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001194' ) $data_identifier = 'HOM05D001194' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 17, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 8, 'sgi' => (int) 7, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356690' $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' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ), 'gf_id' => 'HOM05D001194', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001194' ), 'data_identifier' => 'HOM05D001194', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ) $gf_id = 'HOM05D001194' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001194' ) $data_identifier = 'HOM05D001194' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 17, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 8, 'sgi' => (int) 7, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356690' $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' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ), 'gf_id' => 'HOM05D001194', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001194' ), 'data_identifier' => 'HOM05D001194', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ) $gf_id = 'HOM05D001194' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001194' ) $data_identifier = 'HOM05D001194' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 17, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 8, 'sgi' => (int) 7, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356690' $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' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ), 'gf_id' => 'HOM05D001194', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001194' ), 'data_identifier' => 'HOM05D001194', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ) $gf_id = 'HOM05D001194' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001194' ) $data_identifier = 'HOM05D001194' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 17, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 8, 'sgi' => (int) 7, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356690' $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' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ), 'gf_id' => 'HOM05D001194', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001194' ), 'data_identifier' => 'HOM05D001194', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ) $gf_id = 'HOM05D001194' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001194' ) $data_identifier = 'HOM05D001194' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 17, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 8, 'sgi' => (int) 7, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356690' $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' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ), 'gf_id' => 'HOM05D001194', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001194' ), 'data_identifier' => 'HOM05D001194', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ) $gf_id = 'HOM05D001194' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001194' ) $data_identifier = 'HOM05D001194' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 17, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 8, 'sgi' => (int) 7, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356690' $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' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ), 'gf_id' => 'HOM05D001194', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001194' ), 'data_identifier' => 'HOM05D001194', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ) $gf_id = 'HOM05D001194' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001194' ) $data_identifier = 'HOM05D001194' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 17, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 8, 'sgi' => (int) 7, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356690' $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' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ), 'gf_id' => 'HOM05D001194', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001194' ), 'data_identifier' => 'HOM05D001194', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ) $gf_id = 'HOM05D001194' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001194' ) $data_identifier = 'HOM05D001194' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 17, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 8, 'sgi' => (int) 7, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356690' $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' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ), 'gf_id' => 'HOM05D001194', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001194' ), 'data_identifier' => 'HOM05D001194', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ) $gf_id = 'HOM05D001194' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001194' ) $data_identifier = 'HOM05D001194' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 17, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 8, 'sgi' => (int) 7, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356690' $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' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ), 'gf_id' => 'HOM05D001194', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001194' ), 'data_identifier' => 'HOM05D001194', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ) $gf_id = 'HOM05D001194' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001194' ) $data_identifier = 'HOM05D001194' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 17, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 8, 'sgi' => (int) 7, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356690' $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' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ), 'gf_id' => 'HOM05D001194', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001194' ), 'data_identifier' => 'HOM05D001194', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ) $gf_id = 'HOM05D001194' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001194' ) $data_identifier = 'HOM05D001194' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 17, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 8, 'sgi' => (int) 7, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356690' $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' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ), 'gf_id' => 'HOM05D001194', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001194' ), 'data_identifier' => 'HOM05D001194', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ) $gf_id = 'HOM05D001194' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001194' ) $data_identifier = 'HOM05D001194' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 17, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 8, 'sgi' => (int) 7, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356690' $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' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ), 'gf_id' => 'HOM05D001194', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001194' ), 'data_identifier' => 'HOM05D001194', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ) $gf_id = 'HOM05D001194' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001194' ) $data_identifier = 'HOM05D001194' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 17, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 8, 'sgi' => (int) 7, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356690' $species_info = array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ) $local_species = 'nnu' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ), 'gf_id' => 'HOM05D001194', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001194' ), 'data_identifier' => 'HOM05D001194', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ) $gf_id = 'HOM05D001194' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001194' ) $data_identifier = 'HOM05D001194' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 17, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 8, 'sgi' => (int) 7, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356690' $species_info = array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ) $local_species = 'nnu' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ), 'gf_id' => 'HOM05D001194', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001194' ), 'data_identifier' => 'HOM05D001194', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ) $gf_id = 'HOM05D001194' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001194' ) $data_identifier = 'HOM05D001194' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 17, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 8, 'sgi' => (int) 7, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356690' $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' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ), 'gf_id' => 'HOM05D001194', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001194' ), 'data_identifier' => 'HOM05D001194', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ) $gf_id = 'HOM05D001194' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001194' ) $data_identifier = 'HOM05D001194' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 17, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 8, 'sgi' => (int) 7, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356690' $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' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ), 'gf_id' => 'HOM05D001194', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001194' ), 'data_identifier' => 'HOM05D001194', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ) $gf_id = 'HOM05D001194' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001194' ) $data_identifier = 'HOM05D001194' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 17, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 8, 'sgi' => (int) 7, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356690' $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' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ), 'gf_id' => 'HOM05D001194', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001194' ), 'data_identifier' => 'HOM05D001194', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ) $gf_id = 'HOM05D001194' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001194' ) $data_identifier = 'HOM05D001194' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 17, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 8, 'sgi' => (int) 7, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356690' $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' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ), 'gf_id' => 'HOM05D001194', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001194' ), 'data_identifier' => 'HOM05D001194', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ) $gf_id = 'HOM05D001194' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001194' ) $data_identifier = 'HOM05D001194' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 17, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 8, 'sgi' => (int) 7, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356690' $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' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ), 'gf_id' => 'HOM05D001194', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001194' ), 'data_identifier' => 'HOM05D001194', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ) $gf_id = 'HOM05D001194' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001194' ) $data_identifier = 'HOM05D001194' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 17, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 8, 'sgi' => (int) 7, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356690' $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' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ), 'gf_id' => 'HOM05D001194', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001194' ), 'data_identifier' => 'HOM05D001194', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ) $gf_id = 'HOM05D001194' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001194' ) $data_identifier = 'HOM05D001194' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 17, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 8, 'sgi' => (int) 7, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356690' $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' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ), 'gf_id' => 'HOM05D001194', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001194' ), 'data_identifier' => 'HOM05D001194', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ) $gf_id = 'HOM05D001194' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001194' ) $data_identifier = 'HOM05D001194' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 17, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 8, 'sgi' => (int) 7, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356690' $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' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ), 'gf_id' => 'HOM05D001194', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001194' ), 'data_identifier' => 'HOM05D001194', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ) $gf_id = 'HOM05D001194' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001194' ) $data_identifier = 'HOM05D001194' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 17, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 8, 'sgi' => (int) 7, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356690' $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' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ), 'gf_id' => 'HOM05D001194', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001194' ), 'data_identifier' => 'HOM05D001194', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ) $gf_id = 'HOM05D001194' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001194' ) $data_identifier = 'HOM05D001194' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 17, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 8, 'sgi' => (int) 7, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356690' $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' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ), 'gf_id' => 'HOM05D001194', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001194' ), 'data_identifier' => 'HOM05D001194', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ) $gf_id = 'HOM05D001194' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001194' ) $data_identifier = 'HOM05D001194' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 17, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 8, 'sgi' => (int) 7, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356690' $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' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ), 'gf_id' => 'HOM05D001194', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001194' ), 'data_identifier' => 'HOM05D001194', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ) $gf_id = 'HOM05D001194' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001194' ) $data_identifier = 'HOM05D001194' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 17, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 8, 'sgi' => (int) 7, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356690' $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' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ), 'gf_id' => 'HOM05D001194', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001194' ), 'data_identifier' => 'HOM05D001194', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ) $gf_id = 'HOM05D001194' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001194' ) $data_identifier = 'HOM05D001194' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 17, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 8, 'sgi' => (int) 7, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356690' $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' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ), 'gf_id' => 'HOM05D001194', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001194' ), 'data_identifier' => 'HOM05D001194', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ) $gf_id = 'HOM05D001194' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001194' ) $data_identifier = 'HOM05D001194' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 17, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 8, 'sgi' => (int) 7, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356690' $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' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ), 'gf_id' => 'HOM05D001194', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001194' ), 'data_identifier' => 'HOM05D001194', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ) $gf_id = 'HOM05D001194' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001194' ) $data_identifier = 'HOM05D001194' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 17, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 8, 'sgi' => (int) 7, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356690' $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' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ), 'gf_id' => 'HOM05D001194', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001194' ), 'data_identifier' => 'HOM05D001194', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ) $gf_id = 'HOM05D001194' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001194' ) $data_identifier = 'HOM05D001194' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 17, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 8, 'sgi' => (int) 7, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356690' $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' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ), 'gf_id' => 'HOM05D001194', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001194' ), 'data_identifier' => 'HOM05D001194', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ) $gf_id = 'HOM05D001194' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001194' ) $data_identifier = 'HOM05D001194' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 17, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 8, 'sgi' => (int) 7, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356690' $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' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ), 'gf_id' => 'HOM05D001194', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001194' ), 'data_identifier' => 'HOM05D001194', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ) $gf_id = 'HOM05D001194' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001194' ) $data_identifier = 'HOM05D001194' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 17, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 8, 'sgi' => (int) 7, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356690' $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' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ), 'gf_id' => 'HOM05D001194', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001194' ), 'data_identifier' => 'HOM05D001194', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ) $gf_id = 'HOM05D001194' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001194' ) $data_identifier = 'HOM05D001194' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 17, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 8, 'sgi' => (int) 7, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356690' $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' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ), 'gf_id' => 'HOM05D001194', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001194' ), 'data_identifier' => 'HOM05D001194', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ) $gf_id = 'HOM05D001194' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001194' ) $data_identifier = 'HOM05D001194' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 17, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 8, 'sgi' => (int) 7, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356690' $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' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ), 'gf_id' => 'HOM05D001194', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001194' ), 'data_identifier' => 'HOM05D001194', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ) $gf_id = 'HOM05D001194' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001194' ) $data_identifier = 'HOM05D001194' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 17, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 8, 'sgi' => (int) 7, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356690' $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' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ), 'gf_id' => 'HOM05D001194', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001194' ), 'data_identifier' => 'HOM05D001194', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ) $gf_id = 'HOM05D001194' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001194' ) $data_identifier = 'HOM05D001194' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 17, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 8, 'sgi' => (int) 7, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356690' $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' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ), 'gf_id' => 'HOM05D001194', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001194' ), 'data_identifier' => 'HOM05D001194', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ) $gf_id = 'HOM05D001194' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001194' ) $data_identifier = 'HOM05D001194' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 17, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 8, 'sgi' => (int) 7, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356690' $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' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ), 'gf_id' => 'HOM05D001194', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001194' ), 'data_identifier' => 'HOM05D001194', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ) $gf_id = 'HOM05D001194' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001194' ) $data_identifier = 'HOM05D001194' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 17, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 8, 'sgi' => (int) 7, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356690' $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' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ), 'gf_id' => 'HOM05D001194', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001194' ), 'data_identifier' => 'HOM05D001194', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ) $gf_id = 'HOM05D001194' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001194' ) $data_identifier = 'HOM05D001194' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 17, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 8, 'sgi' => (int) 7, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356690' $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' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ), 'gf_id' => 'HOM05D001194', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001194' ), 'data_identifier' => 'HOM05D001194', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ) $gf_id = 'HOM05D001194' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001194' ) $data_identifier = 'HOM05D001194' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 17, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 8, 'sgi' => (int) 7, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356690' $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' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ), 'gf_id' => 'HOM05D001194', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001194' ), 'data_identifier' => 'HOM05D001194', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ) $gf_id = 'HOM05D001194' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001194' ) $data_identifier = 'HOM05D001194' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 17, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 8, 'sgi' => (int) 7, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356690' $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' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ), 'gf_id' => 'HOM05D001194', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001194' ), 'data_identifier' => 'HOM05D001194', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ) $gf_id = 'HOM05D001194' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001194' ) $data_identifier = 'HOM05D001194' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 17, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 8, 'sgi' => (int) 7, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356690' $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' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ), 'gf_id' => 'HOM05D001194', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001194' ), 'data_identifier' => 'HOM05D001194', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ) $gf_id = 'HOM05D001194' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001194' ) $data_identifier = 'HOM05D001194' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 17, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 8, 'sgi' => (int) 7, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356690' $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' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ), 'gf_id' => 'HOM05D001194', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001194' ), 'data_identifier' => 'HOM05D001194', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ) $gf_id = 'HOM05D001194' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001194' ) $data_identifier = 'HOM05D001194' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 17, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 8, 'sgi' => (int) 7, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356690' $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' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ), 'gf_id' => 'HOM05D001194', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001194' ), 'data_identifier' => 'HOM05D001194', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ) $gf_id = 'HOM05D001194' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001194' ) $data_identifier = 'HOM05D001194' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 17, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 8, 'sgi' => (int) 7, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356690' $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' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ), 'gf_id' => 'HOM05D001194', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001194' ), 'data_identifier' => 'HOM05D001194', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ) $gf_id = 'HOM05D001194' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001194' ) $data_identifier = 'HOM05D001194' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 17, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 8, 'sgi' => (int) 7, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356690' $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' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ), 'gf_id' => 'HOM05D001194', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001194' ), 'data_identifier' => 'HOM05D001194', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ) $gf_id = 'HOM05D001194' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001194' ) $data_identifier = 'HOM05D001194' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 17, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 8, 'sgi' => (int) 7, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356690' $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' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ), 'gf_id' => 'HOM05D001194', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001194' ), 'data_identifier' => 'HOM05D001194', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ) $gf_id = 'HOM05D001194' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001194' ) $data_identifier = 'HOM05D001194' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 17, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 8, 'sgi' => (int) 7, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356690' $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' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ), 'gf_id' => 'HOM05D001194', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001194' ), 'data_identifier' => 'HOM05D001194', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ) $gf_id = 'HOM05D001194' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001194' ) $data_identifier = 'HOM05D001194' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 17, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 8, 'sgi' => (int) 7, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356690' $species_info = array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ) $local_species = 'shi' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ), 'gf_id' => 'HOM05D001194', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001194' ), 'data_identifier' => 'HOM05D001194', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ) $gf_id = 'HOM05D001194' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001194' ) $data_identifier = 'HOM05D001194' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 17, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 8, 'sgi' => (int) 7, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356690' $species_info = array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ) $local_species = 'shi' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ), 'gf_id' => 'HOM05D001194', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001194' ), 'data_identifier' => 'HOM05D001194', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ) $gf_id = 'HOM05D001194' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001194' ) $data_identifier = 'HOM05D001194' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 17, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 8, 'sgi' => (int) 7, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356690' $species_info = array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ) $local_species = 'spa' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ), 'gf_id' => 'HOM05D001194', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001194' ), 'data_identifier' => 'HOM05D001194', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ) $gf_id = 'HOM05D001194' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001194' ) $data_identifier = 'HOM05D001194' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 17, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 8, 'sgi' => (int) 7, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356690' $species_info = array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ) $local_species = 'spa' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ), 'gf_id' => 'HOM05D001194', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001194' ), 'data_identifier' => 'HOM05D001194', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ) $gf_id = 'HOM05D001194' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001194' ) $data_identifier = 'HOM05D001194' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 17, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 8, 'sgi' => (int) 7, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356690' $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' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ), 'gf_id' => 'HOM05D001194', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001194' ), 'data_identifier' => 'HOM05D001194', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ) $gf_id = 'HOM05D001194' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001194' ) $data_identifier = 'HOM05D001194' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 17, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 8, 'sgi' => (int) 7, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356690' $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' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ), 'gf_id' => 'HOM05D001194', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001194' ), 'data_identifier' => 'HOM05D001194', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ) $gf_id = 'HOM05D001194' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001194' ) $data_identifier = 'HOM05D001194' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 17, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 8, 'sgi' => (int) 7, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356690' $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' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ), 'gf_id' => 'HOM05D001194', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001194' ), 'data_identifier' => 'HOM05D001194', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ) $gf_id = 'HOM05D001194' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001194' ) $data_identifier = 'HOM05D001194' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 17, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 8, 'sgi' => (int) 7, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356690' $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' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ), 'gf_id' => 'HOM05D001194', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001194' ), 'data_identifier' => 'HOM05D001194', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ) $gf_id = 'HOM05D001194' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001194' ) $data_identifier = 'HOM05D001194' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 17, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 8, 'sgi' => (int) 7, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356690' $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' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ), 'gf_id' => 'HOM05D001194', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001194' ), 'data_identifier' => 'HOM05D001194', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ) $gf_id = 'HOM05D001194' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001194' ) $data_identifier = 'HOM05D001194' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 17, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 8, 'sgi' => (int) 7, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356690' $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' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ), 'gf_id' => 'HOM05D001194', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001194' ), 'data_identifier' => 'HOM05D001194', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ) $gf_id = 'HOM05D001194' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001194' ) $data_identifier = 'HOM05D001194' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 17, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 8, 'sgi' => (int) 7, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356690' $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' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ), 'gf_id' => 'HOM05D001194', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001194' ), 'data_identifier' => 'HOM05D001194', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ) $gf_id = 'HOM05D001194' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001194' ) $data_identifier = 'HOM05D001194' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 17, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 8, 'sgi' => (int) 7, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356690' $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' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ), 'gf_id' => 'HOM05D001194', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001194' ), 'data_identifier' => 'HOM05D001194', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ) $gf_id = 'HOM05D001194' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001194' ) $data_identifier = 'HOM05D001194' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 17, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 8, 'sgi' => (int) 7, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356690' $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' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ), 'gf_id' => 'HOM05D001194', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001194' ), 'data_identifier' => 'HOM05D001194', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ) $gf_id = 'HOM05D001194' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001194' ) $data_identifier = 'HOM05D001194' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 17, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 8, 'sgi' => (int) 7, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356690' $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' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ), 'gf_id' => 'HOM05D001194', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001194' ), 'data_identifier' => 'HOM05D001194', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ) $gf_id = 'HOM05D001194' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001194' ) $data_identifier = 'HOM05D001194' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 17, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 8, 'sgi' => (int) 7, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356690' $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' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ), 'gf_id' => 'HOM05D001194', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001194' ), 'data_identifier' => 'HOM05D001194', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ) $gf_id = 'HOM05D001194' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001194' ) $data_identifier = 'HOM05D001194' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 17, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 8, 'sgi' => (int) 7, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356690' $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' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ), 'gf_id' => 'HOM05D001194', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001194' ), 'data_identifier' => 'HOM05D001194', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ) $gf_id = 'HOM05D001194' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001194' ) $data_identifier = 'HOM05D001194' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 17, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 8, 'sgi' => (int) 7, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356690' $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' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ), 'gf_id' => 'HOM05D001194', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001194' ), 'data_identifier' => 'HOM05D001194', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ) $gf_id = 'HOM05D001194' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001194' ) $data_identifier = 'HOM05D001194' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 17, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 8, 'sgi' => (int) 7, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356690' $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' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ), 'gf_id' => 'HOM05D001194', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001194' ), 'data_identifier' => 'HOM05D001194', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ) $gf_id = 'HOM05D001194' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001194' ) $data_identifier = 'HOM05D001194' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 17, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 8, 'sgi' => (int) 7, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356690' $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' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ), 'gf_id' => 'HOM05D001194', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001194' ), 'data_identifier' => 'HOM05D001194', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ) $gf_id = 'HOM05D001194' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001194' ) $data_identifier = 'HOM05D001194' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 17, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 8, 'sgi' => (int) 7, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356690' $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' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ), 'gf_id' => 'HOM05D001194', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001194' ), 'data_identifier' => 'HOM05D001194', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ) $gf_id = 'HOM05D001194' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001194' ) $data_identifier = 'HOM05D001194' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 17, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 8, 'sgi' => (int) 7, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356690' $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' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ), 'gf_id' => 'HOM05D001194', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001194' ), 'data_identifier' => 'HOM05D001194', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ) $gf_id = 'HOM05D001194' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001194' ) $data_identifier = 'HOM05D001194' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 17, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 8, 'sgi' => (int) 7, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356690' $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' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ), 'gf_id' => 'HOM05D001194', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001194' ), 'data_identifier' => 'HOM05D001194', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ) $gf_id = 'HOM05D001194' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001194' ) $data_identifier = 'HOM05D001194' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 17, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 8, 'sgi' => (int) 7, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356690' $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' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ), 'gf_id' => 'HOM05D001194', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001194' ), 'data_identifier' => 'HOM05D001194', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ) $gf_id = 'HOM05D001194' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001194' ) $data_identifier = 'HOM05D001194' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 17, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 8, 'sgi' => (int) 7, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356690' $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' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ), 'gf_id' => 'HOM05D001194', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001194' ), 'data_identifier' => 'HOM05D001194', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ) $gf_id = 'HOM05D001194' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001194' ) $data_identifier = 'HOM05D001194' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 17, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 8, 'sgi' => (int) 7, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356690' $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' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ), 'gf_id' => 'HOM05D001194', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001194' ), 'data_identifier' => 'HOM05D001194', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ) $gf_id = 'HOM05D001194' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001194' ) $data_identifier = 'HOM05D001194' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 17, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 8, 'sgi' => (int) 7, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356690' $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' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ), 'gf_id' => 'HOM05D001194', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001194' ), 'data_identifier' => 'HOM05D001194', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ) $gf_id = 'HOM05D001194' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001194' ) $data_identifier = 'HOM05D001194' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 17, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 8, 'sgi' => (int) 7, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356690' $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' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ), 'gf_id' => 'HOM05D001194', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001194' ), 'data_identifier' => 'HOM05D001194', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ) $gf_id = 'HOM05D001194' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001194' ) $data_identifier = 'HOM05D001194' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 17, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 8, 'sgi' => (int) 7, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356690' $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' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ), 'gf_id' => 'HOM05D001194', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001194' ), 'data_identifier' => 'HOM05D001194', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ) $gf_id = 'HOM05D001194' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001194' ) $data_identifier = 'HOM05D001194' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 17, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 8, 'sgi' => (int) 7, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356690' $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' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ), 'gf_id' => 'HOM05D001194', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001194' ), 'data_identifier' => 'HOM05D001194', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ) $gf_id = 'HOM05D001194' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001194' ) $data_identifier = 'HOM05D001194' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 17, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 8, 'sgi' => (int) 7, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356690' $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' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ), 'gf_id' => 'HOM05D001194', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001194' ), 'data_identifier' => 'HOM05D001194', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ) $gf_id = 'HOM05D001194' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001194' ) $data_identifier = 'HOM05D001194' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 17, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 8, 'sgi' => (int) 7, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356690' $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' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ), 'gf_id' => 'HOM05D001194', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001194' ), 'data_identifier' => 'HOM05D001194', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ) $gf_id = 'HOM05D001194' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001194' ) $data_identifier = 'HOM05D001194' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 17, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 8, 'sgi' => (int) 7, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356690' $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' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ), 'gf_id' => 'HOM05D001194', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001194' ), 'data_identifier' => 'HOM05D001194', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ) $gf_id = 'HOM05D001194' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001194' ) $data_identifier = 'HOM05D001194' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 17, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 8, 'sgi' => (int) 7, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356690' $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' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ), 'gf_id' => 'HOM05D001194', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001194' ), 'data_identifier' => 'HOM05D001194', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ) $gf_id = 'HOM05D001194' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001194' ) $data_identifier = 'HOM05D001194' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 17, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 8, 'sgi' => (int) 7, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356690' $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' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ), 'gf_id' => 'HOM05D001194', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001194' ), 'data_identifier' => 'HOM05D001194', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ) $gf_id = 'HOM05D001194' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001194' ) $data_identifier = 'HOM05D001194' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 17, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 8, 'sgi' => (int) 7, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356690' $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' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ), 'gf_id' => 'HOM05D001194', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001194' ), 'data_identifier' => 'HOM05D001194', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ) $gf_id = 'HOM05D001194' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001194' ) $data_identifier = 'HOM05D001194' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 17, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 8, 'sgi' => (int) 7, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356690' $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' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ), 'gf_id' => 'HOM05D001194', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001194' ), 'data_identifier' => 'HOM05D001194', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ) $gf_id = 'HOM05D001194' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001194' ) $data_identifier = 'HOM05D001194' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 17, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 8, 'sgi' => (int) 7, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356690' $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' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ), 'gf_id' => 'HOM05D001194', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001194' ), 'data_identifier' => 'HOM05D001194', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ) $gf_id = 'HOM05D001194' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001194' ) $data_identifier = 'HOM05D001194' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 17, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 8, 'sgi' => (int) 7, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356690' $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' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ), 'gf_id' => 'HOM05D001194', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001194' ), 'data_identifier' => 'HOM05D001194', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ) $gf_id = 'HOM05D001194' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001194' ) $data_identifier = 'HOM05D001194' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 17, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 8, 'sgi' => (int) 7, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356690' $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' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ), 'gf_id' => 'HOM05D001194', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001194' ), 'data_identifier' => 'HOM05D001194', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ) $gf_id = 'HOM05D001194' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001194' ) $data_identifier = 'HOM05D001194' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 17, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 8, 'sgi' => (int) 7, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356690' $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' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ), 'gf_id' => 'HOM05D001194', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001194' ), 'data_identifier' => 'HOM05D001194', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ) $gf_id = 'HOM05D001194' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001194' ) $data_identifier = 'HOM05D001194' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 17, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 8, 'sgi' => (int) 7, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356690' $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' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ), 'gf_id' => 'HOM05D001194', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001194' ), 'data_identifier' => 'HOM05D001194', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ) $gf_id = 'HOM05D001194' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001194' ) $data_identifier = 'HOM05D001194' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 17, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 8, 'sgi' => (int) 7, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356690' $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' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ), 'gf_id' => 'HOM05D001194', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001194' ), 'data_identifier' => 'HOM05D001194', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ) $gf_id = 'HOM05D001194' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001194' ) $data_identifier = 'HOM05D001194' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 17, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 8, 'sgi' => (int) 7, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356690' $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' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ), 'gf_id' => 'HOM05D001194', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001194' ), 'data_identifier' => 'HOM05D001194', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001194', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '523', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p42170' => 'bna', 'A05p19380' => 'bna', 'A05p27320' => 'bna', 'A05p44050' => 'bna', 'A06p02290' => 'bna', 'A06p26280' => 'bna', 'A08p02540' => 'bna', 'Aa31LG10G3060' => 'aar', 'Aa31LG10G3090' => 'aar', 'Aa31LG5G13620' => 'aar', 'Aa31LG8G8000' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2881' => 'aag', 'Actinidia04567' => 'ach', 'Actinidia08738' => 'ach', 'Actinidia09019' => 'ach', 'Actinidia21741' => 'ach', 'Actinidia25337' => 'ach', 'Actinidia25338' => 'ach', 'Actinidia27270' => 'ach', 'Actinidia32129' => 'ach', 'Actinidia32131' => 'ach', 'Actinidia32132' => 'ach', 'Actinidia34300' => 'ach', 'Actinidia39123' => 'ach', 'Ah.01g004470' => 'amhyb', 'Ah.01g016980' => 'amhyb', 'Ah.13g072660' => 'amhyb', 'AL1G59660' => 'aly', 'AL1G59690' => 'aly', 'AL3G12750' => 'aly', 'AL3G35340' => 'aly', 'Aqoxy3G02032' => 'aox', 'Aqoxy7G01307' => 'aox', 'Aqoxy7G01308' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2JHZ20' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3FEZ81' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86BA7N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9ZGB1X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BTK37R' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C23CI2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D8HU13' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6TDML' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H04EJ4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HDE469' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N6M4TT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SR3KA1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TPI7CH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U81MKX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1VE37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V93RAK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YRZZ7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZQU295' => 'arhy', 'AT1G51720' => 'ath', 'AT1G51745' => 'ath', 'AT3G03140' => 'ath', 'AT3G21295' => 'ath', 'ATR0789G175' => 'atr', 'ATR0789G185' => 'atr', 'ATR0829G126' => 'atr', 'Atru.chr1.3627' => 'acertr', 'Atru.chr1.3631' => 'acertr', 'Atru.chr1.3635' => 'acertr', 'Atru.chr12.2006' => 'acertr', 'Atru.chr12.2007' => 'acertr', 'AUR62005912' => 'cqu', 'AUR62022395' => 'cqu', 'AUR62023909' => 'cqu', 'AUR62028153' => 'cqu', 'AUR62034305' => 'cqu', 'AUR62038337' => 'cqu', 'BcaB02g11052' => 'bca', 'BcaB06g26219' => 'bca', 'BcaB07g33628' => 'bca', 'BcaC01g01291' => 'bca', 'BcaC01g01292' => 'bca', 'BcaC05g28183' => 'bca', 'BcaC05g30523' => 'bca', 'BcaC08g43332' => 'bca', 'BcaC08g43937' => 'bca', 'BcaC09g47728' => 'bca', 'BNapus_Darmor_BZH_scaffold_162p00040' => 'bna', 'BNapus_Darmor_BZH_scaffold_78p00030' => 'bna', 'BolC1t05843H' => 'bol', 'BolC3t17445H' => 'bol', 'BolC3t21349H' => 'bol', 'BolC5t32951H' => 'bol', 'BolC5t35036H' => 'bol', 'BolC6t35794H' => 'bol', 'BolC6t36490H' => 'bol', 'BraA01t04589Z' => 'bra', 'BraA03t13370Z' => 'bra', 'BraA05t20842Z' => 'bra', 'BraA06t23435Z' => 'bra', 'BraA08t32294Z' => 'bra', 'BraSC90t46706Z' => 'bra', 'C03p51620' => 'bna', 'C03p90270' => 'bna', 'C05p42230' => 'bna', 'C05p63670' => 'bna', 'C06p06880' => 'bna', 'C06p13300' => 'bna', 'CAN.G1668.4' => 'can', 'CAN.G303.72' => 'can', 'CAN.G410.38' => 'can', 'CAN.G65.133' => 'can', 'CAN.G773.7' => 'can', 'CANSAT21G2052' => 'cansat', 'CANSAT56G1148' => 'cansat', 'CANSAT56G4545' => 'cansat', 'CARHR041880' => 'chi', 'CARHR041900' => 'chi', 'CARHR077160' => 'chi', 'CARHR097200' => 'chi', 'Carub.0001s4059' => 'cru', 'Carub.0001s4062' => 'cru', 'Carub.0003s0229' => 'cru', 'Carub.0003s2131' => 'cru', 'Ca_04930_v3' => 'car', 'Ca_23293_v3' => 'car', 'Ca_23295_v3' => 'car', 'Ca_23297_v3' => 'car', 'Ca_24453_v3' => 'car', 'Ca_29854_v3' => 'car', 'Cc02_g00410' => 'ccan', 'Cc04_g02210' => 'ccan', 'Cc04_g02260' => 'ccan', 'Cc08_g04270' => 'ccan', 'CDE02G0709' => 'cde', 'CDE05G0449' => 'cde', 'CDE05G1083' => 'cde', 'CDE05G3462' => 'cde', 'CDE11G0653' => 'cde', 'CDE11G0829' => 'cde', 'Cfa003606' => 'cfa', 'Cfa003608' => 'cfa', 'Ciclev10018929m.g' => 'ccl', 'Ciclev10025274m.g' => 'ccl', 'Ciclev10027499m.g' => 'ccl', 'CiPaw.01G227200' => 'cil', 'CiPaw.01G227400' => 'cil', 'CiPaw.02G142100' => 'cil', 'CiPaw.02G142200' => 'cil', 'CiPaw.05G237200' => 'cil', 'CiPaw.06G019900' => 'cil', 'ClCG07G013590' => 'cla', 'ClCG07G013600' => 'cla', 'ClCG09G000530' => 'cla', 'ClCG10G009040' => 'cla', 'COL.COLO4_06389' => 'col', 'COL.COLO4_30602' => 'col', 'COL.COLO4_30608' => 'col', 'Cpa.g.sc131.28' => 'cpa', 'Cpa.g.sc131.29' => 'cpa', 'Cpa.g.sc131.30' => 'cpa', 'Cpa.g.sc131.31' => 'cpa', 'Cpa.g.sc39.55' => 'cpa', 'Cpa.g.sc39.56' => 'cpa', 'CsaV3_3G044030' => 'csa', 'CsaV3_3G044050' => 'csa', 'CsaV3_4G009690' => 'csa', 'CsaV3_7G034920' => 'csa', 'CSS0002183' => 'camsi', 'CSS0009358' => 'camsi', 'CSS0018019' => 'camsi', 'CSS0021774' => 'camsi', 'CSS0036616' => 'camsi', 'CSS0039198' => 'camsi', 'CSS0048118' => 'camsi', 'CSS0050239' => 'camsi', 'DCAR_004253' => 'dca', 'DCAR_010547' => 'dca', 'DCAR_014572' => 'dca', 'DCAR_016175' => 'dca', 'DCAR_016176' => 'dca', 'DCAR_028275' => 'dca', 'DCAR_031424' => 'dca', 'Dinv14630' => 'din', 'Dinv17265' => 'din', 'Dinv29043' => 'din', 'Dinv29044' => 'din', 'Dinv29172' => 'din', 'Dinv30399' => 'din', 'Dinv30401' => 'din', 'Dinv37933' => 'din', 'Dinv37935' => 'din', 'Duzib106G2028' => 'dzi', 'Duzib160G0082' => 'dzi', 'Duzib160G0776' => 'dzi', 'Duzib177G1219' => 'dzi', 'Duzib192G0939' => 'dzi', 'Duzib235G0439' => 'dzi', 'Duzib235G0513' => 'dzi', 'ECA232G0548' => 'eca', 'ECA247G2821' => 'eca', 'EL10Ac3g05096' => 'bvu', 'EL10Ac9g21120' => 'bvu', 'EL10Ac9g21131' => 'bvu', 'EL10Ac9g21133' => 'bvu', 'Eucgr.F03102' => 'egr', 'Eucgr.J02887' => 'egr', 'Eucgr.K00094' => 'egr', 'FAN01G1056' => 'fan', 'FAN02G3247' => 'fan', 'FAN02G4259' => 'fan', 'FAN03G3016' => 'fan', 'FAN05G2170' => 'fan', 'FAN05G2672' => 'fan', 'FAN09G1927' => 'fan', 'FAN09G4892' => 'fan', 'FAN10G1232' => 'fan', 'FAN10G2575' => 'fan', 'FAN14G3355' => 'fan', 'FAN14G3358' => 'fan', 'FvH4_6g32930' => 'fve', 'FvH4_6g32960' => 'fve', 'FvH4_7g33620' => 'fve', 'Glyma.01G229500' => 'gma', 'Glyma.07G012500' => 'gma', 'Glyma.07G012700' => 'gma', 'Glyma.08G196200' => 'gma', 'Glyma.08G196400' => 'gma', 'Glyma.09G152800' => 'gma', 'Glyma.11G012300' => 'gma', 'Glyma.11G092700' => 'gma', 'Glyma.12G019000' => 'gma', 'Gohir.A02G139300' => 'ghi', 'Gohir.A05G133600' => 'ghi', 'Gohir.A09G080600' => 'ghi', 'Gohir.A10G062100' => 'ghi', 'Gohir.A10G062200' => 'ghi', 'Gohir.A13G155200' => 'ghi', 'Gohir.D03G050000' => 'ghi', 'Gohir.D05G135500' => 'ghi', 'Gohir.D09G080600' => 'ghi', 'Gohir.D10G063800' => 'ghi', 'Gohir.D10G063900' => 'ghi', 'Gohir.D13G160000' => 'ghi', 'Gorai.003G051500' => 'gra', 'Gorai.006G096200' => 'gra', 'Gorai.009G139300' => 'gra', 'Gorai.011G067700' => 'gra', 'Gorai.011G067800' => 'gra', 'Gorai.013G180600' => 'gra', 'GSVIVG01016891001' => 'vvi', 'GSVIVG01016893001' => 'vvi', 'GSVIVG01016894001' => 'vvi', 'GSVIVG01024445001' => 'vvi', 'HanXRQChr02g0031511' => 'han', 'HanXRQChr04g0095981' => 'han', 'HanXRQChr09g0276311' => 'han', 'HanXRQChr10g0306751' => 'han', 'HanXRQChr14g0462991' => 'han', 'Haze_00595' => 'cav', 'Haze_15917' => 'cav', 'Haze_15919' => 'cav', 'Hma1.2p1_0132F.1_g060700' => 'hma', 'Hma1.2p1_0291F.1_g115460' => 'hma', 'Hma1.2p1_0388F.1_g142150' => 'hma', 'Hma1.2p1_0758F.1_g213610' => 'hma', 'Hma1.2p1_0979F.1_g243540' => 'hma', 'HPP92_001515' => 'vpl', 'HPP92_002456' => 'vpl', 'HPP92_020813' => 'vpl', 'HPP92_020814' => 'vpl', 'HPP92_023231' => 'vpl', 'Hund00742' => 'sun', 'Hund07662' => 'sun', 'Hund09771' => 'sun', 'Hund09772' => 'sun', 'Lalb_Chr04g0263101' => 'lal', 'Lalb_Chr04g0263121' => 'lal', 'Lalb_Chr05g0211321' => 'lal', 'Lalb_Chr09g0320311' => 'lal', 'Lalb_Chr14g0372891' => 'lal', 'Lalb_Chr14g0372901' => 'lal', 'Lalb_Chr16g0376631' => 'lal', 'Lalb_Chr22g0351691' => 'lal', 'Lalb_Chr25g0280541' => 'lal', 'Lj3C889T18' => 'lonja', 'Lj3g0000235' => 'lja', 'Lj3g0001136' => 'lja', 'Lj3g0009108' => 'lja', 'Lj3g0016787' => 'lja', 'Lj5A49T38' => 'lonja', 'Lj5A50T63' => 'lonja', 'Lj8A324T106' => 'lonja', 'LjContig00222g0017614' => 'lja', 'Lsat_1_v5_gn_1_36500' => 'lsa', 'Lsat_1_v5_gn_4_96000' => 'lsa', 'Lsat_1_v5_gn_6_1001' => 'lsa', 'Lsat_1_v5_gn_6_760' => 'lsa', 'Lsat_1_v5_gn_6_840' => 'lsa', 'Lsat_1_v5_gn_8_62140' => 'lsa', 'Manes.04G137500' => 'mes', 'Manes.08G164300' => 'mes', 'Manes.09G124100' => 'mes', 'Manes.11G028900' => 'mes', 'Mapoly0010s0062' => 'mpo', 'MBI04_g06218_MAGBIO' => 'mbi', 'MBI04_g06219_MAGBIO' => 'mbi', 'MD01G1233800' => 'mdo', 'MD07G1305900' => 'mdo', 'MD09G1196200' => 'mdo', 'MD09G1196400' => 'mdo', 'MD17G1176900' => 'mdo', 'MD17G1177000' => 'mdo', 'MD17G1177200' => 'mdo', 'Medtr1g021885' => 'mtr', 'Medtr4g077550' => 'mtr', 'Medtr5g007980' => 'mtr', 'Medtr8g015580' => 'mtr', 'Medtr8g015600' => 'mtr', 'MELO3C013030.2' => 'cme', 'MELO3C013031.2' => 'cme', 'MELO3C016073.2' => 'cme', 'MELO3C024404.2' => 'cme', 'Migut.D00978' => 'egut', 'Migut.D00980' => 'egut', 'Migut.F00103' => 'egut', 'Migut.I00996' => 'egut', 'MSTRG.11007' => 'ama', 'MSTRG.22605' => 'ama', 'MSTRG.22608' => 'ama', 'MSTRG.26935' => 'ama', 'MSTRG.4759' => 'ama', 'MSTRG.8580' => 'ama', 'Nitab4.5_0000115g0340' => 'nta', 'Nitab4.5_0000316g0210' => 'nta', 'Nitab4.5_0000543g0040' => 'nta', 'Nitab4.5_0000543g0050' => 'nta', 'Nitab4.5_0001543g0050' => 'nta', 'Nitab4.5_0004848g0070' => 'nta', 'Nitab4.5_0006071g0040' => 'nta', 'Nitab4.5_0008112g0010' => 'nta', 'Nitab4.5_0012685g0010' => 'nta', 'Nn1g01984' => 'nnu', 'Nn1g06230' => 'nnu', 'Nn2g15445' => 'nnu', 'Nn3g19284' => 'nnu', 'Nn6g35405' => 'nnu', 'Nn6g35406' => 'nnu', 'Nn8g38927' => 'nnu', 'Oeu002522.1' => 'oeu', 'Oeu009830.1' => 'oeu', 'Oeu023782.1' => 'oeu', 'Oeu023784.1' => 'oeu', 'Oeu023785.1' => 'oeu', 'Oeu023786.1' => 'oeu', 'Oeu026529.1' => 'oeu', 'Oeu026530.1' => 'oeu', 'Oeu026531.1' => 'oeu', 'Oeu026532.1' => 'oeu', 'Oeu038596.1' => 'oeu', 'Oeu038841.1' => 'oeu', 'Oeu038842.1' => 'oeu', 'Oeu039980.1' => 'oeu', 'Oeu039981.1' => 'oeu', 'Oeu039983.2' => 'oeu', 'Oeu061064.2' => 'oeu', 'Os01g0558200' => 'osa', 'Os01g0558500' => 'osa', 'Os02g0478050' => 'osa', 'Os02g0700000' => 'osa', 'Peaxi162Scf00038g01230' => 'pax', 'Peaxi162Scf00087g00133' => 'pax', 'Peaxi162Scf00815g00238' => 'pax', 'Peaxi162Scf01650g00046' => 'pax', 'PGR102G0345' => 'pgr', 'PGR102G2826' => 'pgr', 'PGR142G0974' => 'pgr', 'PGSC0003DMG400000539' => 'stu', 'PGSC0003DMG400002598' => 'stu', 'PGSC0003DMG400009302' => 'stu', 'PGSC0003DMG402006819' => 'stu', 'PGSC0003DMG402027032' => 'stu', 'Phvul.002G037800' => 'pvu', 'Phvul.010G141900' => 'pvu', 'Phvul.010G142000' => 'pvu', 'Phvul.010G142200' => 'pvu', 'Phvul.011G021400' => 'pvu', 'Potri.001G193600' => 'ptr', 'Potri.001G193900' => 'ptr', 'Potri.001G199600' => 'ptr', 'Potri.003G045600' => 'ptr', 'Potri.013G081400' => 'ptr', 'Potri.019G048100' => 'ptr', 'Pp3c14_22460' => 'ppa', 'Pp3c1_36440' => 'ppa', 'Pp3c2_4200' => 'ppa', 'PRCOL_00003219' => 'pco', 'Prupe.2G324000' => 'ppe', 'Prupe.3G052600' => 'ppe', 'Prupe.3G052800' => 'ppe', 'Psat2g188000' => 'psa', 'Psat4g194400' => 'psa', 'Psat4g194520' => 'psa', 'Psat7g152400' => 'psa', 'Psat7g171440' => 'psa', 'PSO063G0908' => 'pso', 'PSO063G1381' => 'pso', 'PSO063G4370' => 'pso', 'PSO675G8437' => 'pso', 'PSO717G0001' => 'pso', 'PSO782G2051' => 'pso', 'PSO832G0553' => 'pso', 'PSO832G2057' => 'pso', 'QL05p015783' => 'qlo', 'QL05p015826' => 'qlo', 'QL09p025767' => 'qlo', 'RcHm_v2.0_Chr1g0383861' => 'rch', 'RcHm_v2.0_Chr2g0142441' => 'rch', 'RcHm_v2.0_Chr2g0142481' => 'rch', 'RcHm_v2.0_Chr2g0142511' => 'rch', 'Rhsim03G0220600' => 'rsi', 'Rhsim08G0231000' => 'rsi', 'Rhsim08G0231400' => 'rsi', 'Rhsim08G0238500' => 'rsi', 'Rhsim11G0027300' => 'rsi', 'Sabra01G0135400' => 'sbr', 'Sabra01G0156300' => 'sbr', 'Sabra03G0020700' => 'sbr', 'Sabra19G0057700' => 'sbr', 'SalBow4G0864' => 'sbo', 'SalBow6G0245' => 'sbo', 'Sc12g0009870' => 'sci', 'Sc12g0009880' => 'sci', 'Sc12g0009890' => 'sci', 'Sc12g0009910' => 'sci', 'Sc13g0010810' => 'sci', 'Sed0000220' => 'sed', 'Sed0001313' => 'sed', 'Sed0001910' => 'sed', 'Sed0008718' => 'sed', 'Sed0012613' => 'sed', 'Sed0014756' => 'sed', 'Sed0016739' => 'sed', 'Sed0023550' => 'sed', 'SEGI_11676' => 'sgi', 'SEGI_14715' => 'sgi', 'SEGI_14816' => 'sgi', 'SEGI_20046' => 'sgi', 'SEGI_25027' => 'sgi', 'SEGI_39417' => 'sgi', 'SEGI_40504' => 'sgi', 'SGA_v2.0_scaffold44G16882' => 'sas', 'SGA_v2.0_scaffold45G16989' => 'sas', 'SGA_v2.0_scaffold4G02036' => 'sas', 'SGA_v2.0_scaffold71G23749' => 'sas', 'SGA_v2.0_scaffold71G23755' => 'sas', 'SHI02409' => 'shi', 'SHI02449' => 'shi', 'SHI02453' => 'shi', 'SHI11176' => 'shi', 'SMO119G0344' => 'smo', 'SMO163G0008' => 'smo', 'SMO347G0060' => 'smo', 'Solyc01g014360.1' => 'sly', 'Solyc01g068210.3' => 'sly', 'Solyc03g096880.4' => 'sly', 'Solyc03g121320.3' => 'sly', 'Solyc06g072820.3' => 'sly', 'Sopen01g030150' => 'spe', 'Sopen03g027630' => 'spe', 'Sopen03g040130' => 'spe', 'Sopen06g029200' => 'spe', 'Sopen08g024670' => 'spe', 'Sp1g38360' => 'spa', 'Sp1g38400' => 'spa', 'Sp3g02180' => 'spa', 'Sp3g19340' => 'spa', 'TAR374G0146' => 'tar', 'TAR383G0515' => 'tar', 'TAR383G0892' => 'tar', 'TAR626G0784' => 'tar', 'TAR626G1853' => 'tar', 'TAR629G3215' => 'tar', 'TAR636G2368' => 'tar', 'THA.LOC104802917' => 'tha', 'THA.LOC104805919' => 'tha', 'THA.LOC104810562' => 'tha', 'THA.LOC104817936' => 'tha', 'THA.LOC104817938' => 'tha', 'THA.LOC104827221' => 'tha', 'Thecc.02G171200' => 'tca', 'Thecc.05G207300' => 'tca', 'Thecc.05G208200' => 'tca', 'Thecc.06G107500' => 'tca', 'Thecc.06G107800' => 'tca', 'Thhalv10011307m.g' => 'esa', 'Thhalv10011312m.g' => 'esa', 'Thhalv10020126m.g' => 'esa', 'Thhalv10020246m.g' => 'esa', 'TPR.G37884' => 'tpr', 'TPR.G39947' => 'tpr', 'TPR.G8408' => 'tpr', 'TPR.G8747' => 'tpr', 'TPR.G8761' => 'tpr', 'TWI32G1253' => 'twi', 'TWI34G0064' => 'twi', 'TWI75G1010' => 'twi', 'TWI79G0629' => 'twi', 'TWI79G1226' => 'twi', 'unitig_0.g2431' => 'ugi', 'unitig_52.g17694' => 'ugi', 'unitig_748.g7452' => 'ugi', 'unitig_85.g27208' => 'ugi', 'unitig_92.g28231' => 'ugi', 'vmacro06501' => 'vma', 'vmacro10183' => 'vma', 'vmacro18821' => 'vma', 'vmacro18823' => 'vma', 'VMungo0331G0168' => 'vmu', 'VMungo0331G0192' => 'vmu', 'VMungo0331G0238' => 'vmu', 'VMungo1127G0847' => 'vmu', 'Zm00001eb162250' => 'zma', 'Zm00001eb162270' => 'zma', 'Zm00001eb162300' => 'zma', 'Zm00001eb188160' => 'zma', 'Zm00001eb251630' => 'zma', 'Zm00001eb297240' => 'zma', 'Zm00001eb345410' => 'zma', 'Zm00001eb356690' => 'zma' ) $gf_id = 'HOM05D001194' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001194' ) $data_identifier = 'HOM05D001194' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 12, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 6, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 7, 'din' => (int) 9, 'dzi' => (int) 7, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 9, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 5, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 17, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 8, 'sgi' => (int) 7, 'sas' => (int) 5, 'shi' => (int) 4, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 7, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 8 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356690' $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